Comparative Microbiomes of the Respiratory Tract and Joints of Feedlot Cattle Mortalities

Li, Chunli; Zaheer, Rahat; Kinnear, Andrea; Jelinski, Murray; McAllister, Tim A.

doi:10.3390/microorganisms10010134

Cited by 7 publications

(5 citation statements)

References 37 publications

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“…were more prevalent among lung tissues (38%) than nasal swabs (35%). This result is in complete agreement with those reported in previous studies conducted in Europe (60 and 24.4%, respectively) [ 54 ] and Canada (36 and 8.8%, respectively) [ 68 ], but it was in contrast with previous studies conducted in Europe, where Mycoplasma spp. were more prevalent among nasal swabs than lung tissues [ 69 ].…”

Section: Discussionsupporting

confidence: 93%

Prevalence and Antimicrobial Susceptibility of Bovine Mycoplasma Species in Egypt

Ammar

El-Hamid

Mohamed

et al. 2022

Biology

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Among many bovine Mycoplasma species (spp.), Mycoplasma bovis is recognized as a significant causative agent of respiratory diseases in cattle. In recent years, resistant M. bovis isolates, especially to fluoroquinolones, have been reported globally as a result of the extensive usage of antimicrobials in the treatment of bovine pneumonia. Therefore, the aim of this study is to investigate the prevalence and antimicrobial susceptibility patterns of bovine Mycoplasma spp. isolated from the respiratory tracts of cattle in Egypt and to assess the fluoroquinolones resistance in the recovered mycoplasma isolates via broth microdilution and conventional PCR techniques. Conventional phenotypic methods identified 128 mycoplasma isolates (32%) from 400 different samples, with M. bovis being the predominant spp. (61%), followed by M. bovirhinis (15%). Of note, mycoplasma isolates were rarely isolated from total healthy lung tissues (7/55, 12.7%), but they were frequently isolated from pneumonic lungs (31/45, 68.9%). All the examined mycoplasma isolates (n = 76) were sensitive to tilmicosin, tylosin, tulathromycin, spiramycin, and spectinomycin (100% each), while 60.5% and 43.4% of the examined isolates had high minimum inhibitory concentration (MIC) values to enrofloxacin and doxycycline, respectively. Three and two mycoplasma isolates with high enrofloxacin MICs were confirmed to be M. bovis and M. bovirhinis, respectively, by PCR assays. All molecularly confirmed mycoplasma isolates (n = 5) were positive for the gyrA gene (100%); meanwhile, three isolates (60%) were positive for the parC gene. In conclusion, our findings revealed alarming resistance to enrofloxacin and doxycycline antibiotics; thus, antimicrobial usage must be restricted and molecular techniques can help in the rapid detection of the resistant strains.

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Section: Discussionsupporting

confidence: 93%

Prevalence and Antimicrobial Susceptibility of Bovine Mycoplasma Species in Egypt

Ammar

El-Hamid

Mohamed

et al. 2022

Biology

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“…These data indicate that the bacterial profiles of the lung lavage samples are significantly different in taxa diversity when compared to the nasal and tonsil samples. While lower alpha diversity is typically associated with disease, previous research has reported a similar lower diversity of the lung compared to other respiratory tract locations of post-weaned beef calves (Nicola et al, 2017) and feedlot cattle (McMullen et al, 2020a;Li et al, 2022). This suggests that the lower diversity of the lung lavage samples, as reported in the data presented herein, is not associated with disease.…”

Section: Alpha and Beta Diversitiessupporting

confidence: 71%

Probiotics in milk replacer affect the microbiome of the lung in neonatal dairy calves

McDaneld,

Eicher,

Dickey

et al. 2024

Front. Microbiol.

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IntroductionProbiotics have been investigated for their many health benefits and impact on the microbiota of the gut. Recent data have also supported a gut–lung axis regarding the bacterial populations (microbiomes) of the two locations; however, little research has been performed to determine the effects of oral probiotics on the microbiome of the bovine respiratory tract. We hypothesized that probiotic treatment would result in changes in the lung microbiome as measured in lung lavage fluid. Our overall goal was to characterize bacterial populations in the lungs of calves fed probiotics in milk replacer and dry rations from birth to weaning.MethodsA group of 20 dairy calves was split into two treatment groups: probiotic (TRT; N = 10, milk replacer +5 g/d probiotics; Bovamine Dairy, Chr. Hansen, Inc., Milwaukee, WI) and control (CON; N = 10, milk replacer only). On day 0, birth weight was obtained, and calves were provided colostrum as per the dairy SOP. On day 2, probiotics were added to the milk replacer of the treated group and then included in their dry ration. Lung lavages were performed on day 52 on five random calves selected from each treatment group. DNA was extracted from lavage fluid, and 16S ribosomal RNA (rRNA) gene hypervariable regions 1–3 were amplified by PCR and sequenced using next-generation sequencing (Illumina MiSeq) for the identification of the bacterial taxa present. Taxa were classified into both operational taxonomic units (OTUs) and amplicon sequence variants (ASVs).ResultsOverall, the evaluation of these samples revealed that the bacterial genera identified in the lung lavage samples of probiotic-fed calves as compared to the control calves were significantly different based on the OTU dataset (p < 0.05) and approached significance for the ASV dataset (p < 0.06). Additionally, when comparing the diversity of taxa in lung lavage samples to nasal and tonsil samples, taxa diversity of lung samples was significantly lower (p < 0.05).DiscussionIn conclusion, analysis of the respiratory microbiome in lung lavage samples after probiotic treatment provides insight into the distribution of bacterial populations in response to oral probiotics and demonstrates that oral probiotics affect more than the gut microbiome.

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“…Many studies report slightly different results for observed sequence variants, including observed operational taxonomic units (OTUs) (Holman et al, 2015), species (Zeineldin et al, 2017;McMullen et al, 2019), amplicon sequence variants (ASVs), and the number of reads (Lima et al, 2016), which can make comparisons among studies difficult. Furthermore, previous results have varied regarding differentially abundant and significantly enriched bacterial taxa as well (Lima et al, 2016;Zeineldin et al, 2017;McMullen et al, 2020;Zeineldin et al, 2020;Raabis et al, 2021;Centeno-Martinez et al, 2022;Li et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Effect of bovine respiratory disease on the respiratory microbiome: a meta-analysis

Howe,

Kegley,

Powell

et al. 2023

Front. Cell. Infect. Microbiol.

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BackgroundBovine respiratory disease (BRD) is the most devastating disease affecting beef and dairy cattle producers in North America. An emerging area of interest is the respiratory microbiome’s relationship with BRD. However, results regarding the effect of BRD on respiratory microbiome diversity are conflicting.ResultsTo examine the effect of BRD on the alpha diversity of the respiratory microbiome, a meta-analysis analyzing the relationship between the standardized mean difference (SMD) of three alpha diversity metrics (Shannon’s Diversity Index (Shannon), Chao1, and Observed features (OTUs, ASVs, species, and reads) and BRD was conducted. Our multi-level model found no difference in Chao1 and Observed features SMDs between calves with BRD and controls. The Shannon SMD was significantly greater in controls compared to that in calves with BRD. Furthermore, we re-analyzed 16S amplicon sequencing data from four previously published datasets to investigate BRD’s effect on individual taxa abundances. Additionally, based on Bray Curtis and Jaccard distances, health status, sampling location, and dataset were all significant sources of variation. Using a consensus approach based on RandomForest, DESeq2, and ANCOM-BC2, we identified three differentially abundant amplicon sequence variants (ASVs) within the nasal cavity, ASV5_Mycoplasma, ASV19_Corynebacterium, and ASV37_Ruminococcaceae. However, no ASVs were differentially abundant in the other sampling locations. Moreover, based on SECOM analysis, ASV37_Ruminococcaceae had a negative relationship with ASV1_Mycoplasma_hyorhinis, ASV5_Mycoplasma, and ASV4_Mannheimia. ASV19_Corynebacterium had negative relationships with ASV1_Mycoplasma_hyorhinis, ASV4_Mannheimia, ASV54_Mycoplasma, ASV7_Mycoplasma, and ASV8_Pasteurella.ConclusionsOur results confirm a relationship between bovine respiratory disease and respiratory microbiome diversity and composition, which provide additional insight into microbial community dynamics during BRD development. Furthermore, as sampling location and sample processing (dataset) can also affect results, consideration should be taken when comparing results across studies.

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Comparative Microbiomes of the Respiratory Tract and Joints of Feedlot Cattle Mortalities

Cited by 7 publications

References 37 publications

Prevalence and Antimicrobial Susceptibility of Bovine Mycoplasma Species in Egypt

Prevalence and Antimicrobial Susceptibility of Bovine Mycoplasma Species in Egypt

Probiotics in milk replacer affect the microbiome of the lung in neonatal dairy calves

Effect of bovine respiratory disease on the respiratory microbiome: a meta-analysis

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